They have such a large discography, we should see an interesting range of picks. I myself am more fond of their early years, though I still haven't heard everything they've put out. I'm kind of hoping these lists will give me some indication of what album I should pick up next. Anyway, here's my top ten:

My fave band of all time... I cannot choose just one song, the Crystal Logic album is absolutelly perfect, Open The Gates and The Deluge the same. Choosing three songs from CL I have to say:
1) Necropolis - for emotional impact
2) Crystal Logic - for the incredibile and unreachable songwriting
3) Flaming Metal System (although it was not present in the original version) - for the catchy and anthemic attitude